Have a head scratcher that I cannot quite figure out.
In opengrok when you are looking at a file and turn on the annotate feature / link, you see columns for changeset history, search for this changelist, and the user id or email address of the submitter. My question is in regards to this last part, the user id or email address.
Right now the hyperlink points to ...
http://www.myserver.org/viewProfile.jspa?username=jsmith%40acme.com
How could one go about customizing this?
This is for opengrok with mercurial as well.
Thanks in advance.
The value can be configured via -B flag.
https://github.com/OpenGrok/OpenGrok/blob/master/src/org/opensolaris/opengrok/index/CommandLineOptions.java#L77
If you are indexing with the 'OpenGrok' script file (the file you run when start indexing) you can edit it and add this option in CommonInvocation() function.
Here is a diff example of my change:
--- opengrok-0.12.1.5/bin/OpenGrok.orig 2016-02-18 19:16:31.504272867 +0200
+++ opengrok-0.12.1.5/bin/OpenGrok 2016-02-18 19:17:29.167968433 +0200
## -148,6 +148,7 ##
# operating systems, if you have any reasonably generic
# improvements please feel free to submit a patch.
+ MY_BASE_URL="http://myCompanyUrl.com?q="
OPENGROK_INSTANCE_BASE="${OPENGROK_INSTANCE_BASE:-/var/opengrok}"
## -808,6 +809,7 ##
${CTAGS_OPTIONS_FILE:+-o} ${CTAGS_OPTIONS_FILE} \
${OPENGROK_FLUSH_RAM_BUFFER_SIZE} ${SKIN} ${LEADING_WILDCARD} \
${READ_XML_CONF} \
+ -B ${MY_BASE_URL} \
"${#}"
}
Looks like it is hard-coded ;(
https://github.com/OpenGrok/OpenGrok/blob/master/src/org/opensolaris/opengrok/configuration/Configuration.java#L227
So, probably the right way to do this is to provide your own Configuration implementation.
Another possible workaround is just to disable 'wrong' links -- they are not very useful in any case.. Something like this in source/default/style.css:
.blame .a { /* author name "column" (annotation) */
text-align: center;
pointer-events: none;
cursor: default;
}
#revisions td:nth-child(4) {
pointer-events: none;
cursor: default;
}
Related
I have a problem figuring out how to make the input directive only select all {samples} files in the rule below.
rule MarkDup:
input:
expand("Outputs/MergeBamAlignment/{samples}_{lanes}_{flowcells}.merged.bam", zip,
samples=samples['sample'],
lanes=samples['lane'],
flowcells=samples['flowcell']),
output:
bam = "Outputs/MarkDuplicates/{samples}_markedDuplicates.bam",
metrics = "Outputs/MarkDuplicates/{samples}_markedDuplicates.metrics",
shell:
"gatk --java-options -Djava.io.tempdir=`pwd`/tmp \
MarkDuplicates \
$(echo ' {input}' | sed 's/ / --INPUT /g') \
-O {output.bam} \
--VALIDATION_STRINGENCY LENIENT \
--METRICS_FILE {output.metrics} \
--MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 200000 \
--CREATE_INDEX true \
--TMP_DIR Outputs/MarkDuplicates/tmp"
Currently it will create correctly named output files, but it selects all files that match the pattern based on all wildcards. So I'm perhaps halfway there. I tried changing {samples} to {{samples}} in the input directive as such:
expand("Outputs/MergeBamAlignment/{{samples}}_{lanes}_{flowcells}.merged.bam", zip,
lanes=samples['lane'],
flowcells=samples['flowcell']),`
but this broke the previous rule somehow. So the solution is something like
input:
"{sample}_*.bam"
But clearly this doesn't work.
Is it possible to collect all files that match {sample}_*.bam with a function and use that as input? And if so, will the function still work with $(echo ' {input}' etc...) in the shell directive?
If you just want all the files in the directory, you can use a lambda function
from glob import glob
rule MarkDup:
input:
lambda wcs: glob('Outputs/MergeBamAlignment/%s*.bam' % wcs.samples)
output:
bam="Outputs/MarkDuplicates/{samples}_markedDuplicates.bam",
metrics="Outputs/MarkDuplicates/{samples}_markedDuplicates.metrics"
shell:
...
Just be aware that this approach can't do any checking for missing files, since it will always report that the files needed are the files that are present. If you do need confirmation that the upstream rule has been executed, you can have the previous rule touch a flag, which you then require as input to this rule (though you don't actually use the file for anything other than enforcing execution order).
If I understand correctly, zip needs to be applied only to {lane} and {flowcells} and not to {samples}. In that case, use two expand instances can achieve that.
input:
expand(expand("Outputs/MergeBamAlignment/{{samples}}_{lanes}_{flowcells}.merged.bam",
zip, lanes=samples['lane'], flowcells=samples['flowcell']),
samples=samples['sample'])
PS: output.tmp file uses {sample} instead of {samples}. Typo?
My os:debian8.
uname -a
Linux debian 3.16.0-4-amd64 #1 SMP Debian 3.16.39-1+deb8u2 (2017-03-07) x86_64 GNU/Linux
Here is my base file.
home
help
variables
compatibility
modelines
searching
selection
markers
indenting
reformatting
folding
tags
makefiles
mapping
registers
spelling
plugins
etc
I want to create a html file as bellow.
home
help
variables
compatibility
modelines
searching
selection
markers
indenting
reformatting
folding
tags
makefiles
mapping
registers
spelling
plugins
etc
Every line was added href and id attributes,whose values are line content pasted .html and line content itself correspondingly.
How to add html attributes and values for all lines quickly with vim and plugins?
sed,awk,sublime text 3 are all welcomed to solve the problem.
$ sed 's:.*:&:' file
home
help
variables
compatibility
modelines
searching
selection
markers
indenting
reformatting
folding
tags
makefiles
mapping
registers
spelling
plugins
etc
if you want to do this in vi itself, no plug-in neccessary
Open the file, type : and insert this line as the command
%s:.*:&
it will make all the substitutions in the file.
sed is the best solution (simple and pretty fast here) if your are sure of the content, if not it need a bit of complexity that is better treated by awk:
awk '
{
# change special char for HTML constraint
Org = URL = HTML = $0
# sample of modification
gsub( / /, "%20", URL)
gsub( /</, "%3C", HTML)
printf( "%s\n", URL, Org, HTML)
}
' YourFile
To complete this easily in Sublime Text, without any plugins added:
Open the base file in Sublime Text
Type Ctrl+Shift+P and in the fuzzy search input type syn html to set the file syntax to HTML.
In the View menu, make sure Word Wrap is toggled off.
Ctrl+A to select all.
Ctrl+Shift+L to break selection into multi-line edit.
Ctrl+C to copy selection into clipboard as multiple lines.
Alt+Shift+W to wrap each line with a tag-- then tap a to convert the default <p> tag into an <a> tag (hit esc to quit out of any context menus that might pop up)
Type a space then href=" -- you should see this being added to every line as they all have cursors. Also you should note that Sublime has automatically closed your quotes for you, so you have href="" with the cursor between the quotes.
ctrl+v -- this is where the magic happens-- your clipboard contains every lines worth of contents, so it will paste each appropriate value into the quotes where the cursor is lying. Then you simply type .html to add the extension.
Use the right arrow to move the cursors outside of the quotes for the href attribute and follow the two previous steps to similarly add an id attribute with the intended ids pasted in.
Voila! You're done.
Multi-line editing is very powerful as you learn how to combine it with other keyboard shortcuts. It has been a huge improvement in my workflow. If you have any questions please feel free to comment and I'll adjust as needed.
With bash one-liner:
while read v; do printf '%s\n' "$v" "$v" "$v"; done < file
(OR)
while read v; do echo "$v"; done < file
Try this -
awk '{print a$1b$1c$1d}' a='' d='' file
home
help
variables
compatibility
modelines
searching
selection
markers
indenting
reformatting
folding
tags
makefiles
mapping
registers
spelling
plugins
etc
Here I have created 4 variable a,b,c & d which you can edit as per your choice.
OR
while read -r i;do echo ""$i";done < f
home
help
variables
compatibility
To execute it directly in vim:
!sed 's:.*:&:' %
In awk, no regex, no nothing, just print strings around $1s, escaping "s:
$ awk '{print "" $1 ""}' file
home
help
If you happen to have empty lines in there just add /./ before the {:
/./{print ...
list=$(cat basefile.txt)
for val in $list
do
echo ""$val"" >> newfile.html
done
Using bash, you can always make a script or type this into the command line.
This vim replacement pattern handles your base file:
s#^\s*\(.\{-}\)\s*$#\1#
^\s* matches any leading spaces, then
.\{-} captures everything after that, non-greedily — allowing
\s$ to match any trailing spaces.
This avoids giving you stuff like home .
You can also process several base files with vim at once:
vim -c 'bufdo %s#^\s*\(.\{-}\)\s*$#\1# | saveas! %:p:r.html' some.txt more.txt`
bufdo %s#^\s*\(.\{-}\)\s*$#\1# runs the replacement on each buffer loaded into vim,
saveas! %:p:r.html saves each buffer with an html extension, overwriting if necessary,
vim will open and show you the saved more.html, which you can correct as needed, and
you can use :n and :prev to visit some.html.
Something like sed’s probably best for big jobs, but this lets you tweak the conversions in vim right after it’s made them, use :u to undo, etc. Enjoy!
I'm editing a json configuration file, and much of it is similar. I'd like to edit it in hunks, since I was overly eager and made more than one change to my working directory.
I removed the configurations for two pages.
I'd prefer to add the changes to the index (the stage) separately in two separate commits, by adding hunks to them; however....
When I do go to do this; git ends up confusing the lines I remove with lines from the second page's configuration using git add -p config.js and it ends up in several hunks, looking something like this:
# Manual hunk edit mode -- see bottom for a quick guide
## -665,25 +665,30 ## var handlebarTemplateGen = function(loadedContent, filePathsArray) {
}
]
},
+ /*BEGIN: Controller*/
{
- "outputfile":"../../someplace.org/removeMe1.html",
+ "outputfile":"../../someplace.org/removeMe2.html",
"processingOrder": [
{
"view":"views/common/empty.view",
"template":"HeadStart.mustache"
},
+ /*
{
- "view":"views/removeMe1/meta.view",
+ "view":"views/removeMe2/meta.view",
"template":"meta.mustache"
},
+ */
{
- "view":"views/removeMe1/HeadEnd.view",
+ "view":"views/removeMe2/HeadEnd.view",
"template":"HeadEnd.mustache"
},
+ /*
{
"view":"views/common/empty.view",
"template":"SocialMediaShareScripts.mustache"
},
+ */
{
"view":"views/index/navbar.view",
"template":"navbar.mustache"
# ---
# To remove '-' lines, make them ' ' lines (context).
# To remove '+' lines, delete them.
# Lines starting with # will be removed.
...and I've tried about everything, but I can't seem to get just the changes to removeMe1 on the stage without also having the removeMe2 changes come along for the ride.
I tried following the instructions about counting lines when editing manually hunks in joaquin's post here, but when I get to the last one that states that I can't remove the references lines I start to have an issue, since I want to remove a block of code and set the reference lines to - (which I understand you have to replace, not just type in)
There was also a video that was helpful on learning this here, but it didn't really fix my issue; it simply told me about how lines should be counted.
I frequently get the "patch does not apply" error when doing this as well, usually because I turned a reference line into a - line.
Is there a way to split this by spiting hunks into separate commits, or is it just a bad idea to store json config files in git?
What I want:
A command that prints number of added (+) and removed (-) from change log, where the added portion(+) written in green and deleted portion (-) written in red.
What I have currently:
hg log -T {diffstat} prints what I want (+20/-31:) but in black color.
hg log -T "{label('custom.colorcode', diffstat)} \n" prints the entire diffstat (+20/-31:) in green (my custom.colorcode is set to green in .hgrc)
References:
https://www.mercurial-scm.org/repo/hg/help/templates
Can I add custom colors to mercurial command templates?
I don't believe there is a way for Mercurial to automatically parse the diffstat output and to assign colors to parts of it, but you can use a workaround by doing the parsing yourself. E.g. with the following template:
hg log -T '{sub("(.*): (.*)/(.*)", "\\1: \033[0;32m\\2\033[0m/\033[0;31m\\3\033[0m", diffstat)}\n'
Note that this hardcodes ANSI color escapes (32 for green, 31 for red). If you want to do it with labels, this is also possible, but much slower (because diffstat has to be calculated multiple times). This approach can still be useful for other keywords, so I'm explaining it anyway. Here is an example template:
{sub(":.*","",diffstat)}: \
{label("diff.inserted", sub(".*([+][0-9]+).*", "\\1", diffstat))}/\
{label("diff.deleted", sub(".*(-[0-9]+).*", "\\1", diffstat))}
The easiest way to use such a long template is to put it in a file (for example ~/.hgtemplates/diffstat) and then use hg log -T ~/.hgtemplates/diffstat. If a template contains a slash or backslash and corresponds to an existing file, Mercurial will look at the contents of the file instead. Long templates can also be put in the templates section of your .hgrc, e.g.:
[templates]
diffstat = "{sub(":.*","",diffstat)}: \
{label("diff.inserted", sub(".*([+][0-9]+).*", "\\1", diffstat))}/\
{label("diff.deleted", sub(".*(-[0-9]+).*", "\\1", diffstat))}\n"
And can then be used with the corresponding name (e.g. hg log -T diffstat).
I'm using Mercurial (specifically TortoiseHg on Windows) to do version control of VBA code. Anybody who's tried this knows that VBA changes the case of every variable throughout a project whenever any declaration of that variable is changed anywhere in the project (regardless of scope). It makes version control a nightmare.
I would like to ignore case changes in my source code when performing diffs. What is the easiest way to do this? (some option for diff that I'm missing, an external diff utility, something else?)
NOTE: I am not talking about dealing with 'case-insensitive filenames' (yes, I'm talking to you Google...)
You can do that when diffing for your on-screen consumption using the ExtDiff Extension.
[extensions]
hgext.extdiff =
[extdiff]
# add new command that runs GNU diff(1) in case-insensitive mode
cmd.mydiff = diff
opts.mydiff = -i
Then you'd run hg mydiff from the command line. That, of course, requires you have a diff binary installed be it gnu's or other.
However, that's not going to be as helpful as you might like because internally, of course, Mercurial can't ignore case -- it's taking the cryptographic hash of the file contents, and those don't allow for wiggle room. So if you get this set up you'll do hg mydiff, and see no changes, and then do hg commit and see changes all over the place.
So you can make this work on-screen, but not fundamentally.
One option would be to find a visual basic code-cleaner, similar to indent for C-like languages, that normalizes variable case and run that in a mercurial commit hook. Then at least all the code going into source control will be consistent and you can diff across revisions accurately.
If you are okay with having your code in all lower-case, say, then you could employ the encode/decode hooks for this. It would work like this:
[encode]
*.vba = tr A-Z a-z
This will encode the file content in lower-case whenever you do a commit. The diffs are also computed based on the encoded (repository) version of the files.
Consider a file that contains
hello
Changing it in your working copy to
Hello World
will give a diff of
% hg diff
diff --git a/a.txt b/a.txt
--- a/a.txt
+++ b/a.txt
## -1,1 +1,1 ##
-hello
+hello world
Notice how the capital "H" and "W" has been ignored.
I don't really know anything about VBA code, so I'm not 100% sure this solution works for you. But I hope it can be a starting point.
One drawback is that you'll need to set this encode rule for all your repositories. The reposettings extension can help you here.
Here's the solution I have settled on. It is far from ideal, but better than the other alternatives I've considered.
I created an Autohotkey script that does the following:
reverts MS Access files in a repository with detected changes (to .orig files)
reads in the .orig file (the one with the changes)
reads in the existing file (the one already in the repository)
converts the text of both files to lower case
compares the lower case contents of the files
if the files still differ, the .orig file is restored so it may be committed to the repository
if the files are the same (i.e., they differ only in case, the .orig file is deleted because we don't care about those changes)
For files that have actual changes that we care about, I still see the case changes that were made as well. If that results in a lot of noise, I open the file in a comparison tool that allows case-insensitive compares (e.g., kdiff).
It's not a perfect solution, but it removes about 90% of the frustration for me.
Here's my script. Note that the script includes another Autohotkey script, ConsoleApp.ahk, which provides a function named, ConsoleApp_RunWait(). This is a 3rd party script that no longer works very well with 64-bit AHK, so I'm not including it as part of my answer. Any AHK function that executes a command line and returns the output as a string will suffice.
; This script checks an MS Access source directory and reverts all files whose only modifications are to the
; case of the characters within the file.
#Include %A_ScriptDir%\ConsoleApp.ahk
#NoEnv ; Recommended for performance and compatibility with future AutoHotkey releases.
SendMode Input ; Recommended for new scripts due to its superior speed and reliability.
SetWorkingDir %A_ScriptDir% ; Ensures a consistent starting directory.
; Allow for custom path to hg (support for moving to TortoiseHg 2.0)
IniRead hg, %A_ScriptDir%\LocalSettings\Settings.cfg, TortoiseHg, hg_path, hg
if 0 < 1 ; The left side of a non-expression if-statement is always the name of a variable.
{
MsgBox Usage:`n`HgIgnoreCase DirectoryWithFilesToScrub
ExitApp
}
SrcDir = %1%
StringReplace SrcDir, SrcDir, ", , All
StringRight test, SrcDir, 1 ; add trailing slash if necessary
ifnotequal test, \
SrcDir = %SrcDir%\
RestoreOriginals(SrcDir)
RevertCaseChangeModifiedFiles(SrcDir)
RevertCaseChangeModifiedFiles(SrcDir) {
global hg
includes = -I "*.form" -I "*.bas" -I "*.report" -I "*.table"
cmdline = %hg% revert --all %includes%
;Don't revert items that have been removed completely
Loop 3
{
Result := ConsoleApp_RunWait(hg . " status -nrd " . includes, SrcDir)
If (Result)
Break
}
Loop parse, Result, `n, `r
{
if (A_LoopField)
cmdline = %cmdline% -X "%A_LoopField%"
}
Result =
;msgbox %cmdline%
;revert all modified forms, reports, and code modules
Loop 3
{
Result := ConsoleApp_RunWait(cmdline, SrcDir)
If (Result)
Break
}
;MsgBox %Result%
Loop parse, Result, `n, `r
{
StringLeft FileStatus, A_LoopField, 9
If (FileStatus = "reverting")
{
StringMid FName, A_LoopField, 11
FullPath = %SrcDir%%FName%
ToolTip Checking %FullPath%
RestoreIfNotEqual(FullPath, FullPath . ".orig")
}
}
ToolTip
}
RestoreIfNotEqual(FName, FNameOrig) {
FileRead File1, %FName%
FileRead File2, %FNameOrig%
StringLower File1, File1
StringLower File2, File2
;MsgBox %FName%`n%FNameOrig%
If (File1 = File2)
FileDelete %FNameOrig%
Else
FileMove %FNameOrig%, %FName%, 1
}
RestoreOriginals(SrcDir) {
Loop %SrcDir%*.orig
{
;MsgBox %A_LoopFileLongPath%`n%NewName%
NewName := SubStr(A_LoopFileLongPath, 1, -5)
FileMove %A_LoopFileLongPath%, %NewName%, 1
}
while FileExist(SrcDir . "*.orig")
Sleep 10
}